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It will help in preparing for the exam to read:
Chapter 19p.450-451, 456-472
Chapter 20p. 473-484
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Comparative Genomics: The study of genome conservation
and variation among organisms
Chromosome numberChromosome morphology
Gene number
Genome sizeGene order
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Measures of Genome Size
C value : amount of DNA in the haploid genome, generally measured in picograms or in base pairs (Kb or Mb)
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Range of C Values in Prokaryotes
Taxon Genome Size (Kb) Ratio
Bacteria 580 - 13,200 23 Mollicutes 580 - 2,200 4 Gram negatives 650 - 9,500 15 Gram positives 1,600 - 11,600 7 Cyanobacteria 3,100 - 13,200 4Archaea 1,600 - 4,100 3
~ 20 fold range in genome size
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Genome Size (x 106 bp)
1000
2000
3000
4000
5000
GeneNumber
Gene Number and Genome Size in 12 CompletelySequenced Bacterial Species
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C value : So, what about eukaryotes?
• In general, more DNA
• Much greater variation in genome size• 80,000 fold range across eukaryotes
• Largest range observed among unicellular protists (20,000 fold)
• 3,000 fold range in animals
• No relationship between c value and organismal complexity:
the c value paradox
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Species C value (Kb)Saccharomyces cerevisiae 12,000Caenorhabditi elegans 80,000Drosophila melanogaster 180,000Strongylocentrotus purpuratus 870,000Gallus domesticus 1,200,000Canis familiaris 2,900,000Rattus norvegicus 2,900,000Xenopus laevis 3,100,000Homo sapiens 3,600,000Nicotiana tabacum 3,800,000Ambystoma tigrinum 32,000,000Pinus resinosa 68,000,000Lepidosiren paradoxa 120,000,000Ophioglossum petiolatum 160,000,000Amoeba dubia 690,000,000
C values from eukaryotic organisms ranked by genome size
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Genome size and amount of heterochromatin
98% of variance explained
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Genic Fraction vs Genome Size
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Human
Reptile
Salamander
Salamander Genome….BIG!
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Make BAC Library 36, 864 clones
PCR Screen for BACs that contain genes
Sequence 16 BACs
Clean
Assemble
Annotate
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AssemblyTotal Reads for Clustering
(767,157)
PaCE
Total PaCE Clusters (420,326)
Single Sequence Clusters (362,760)
Multi Sequence Clusters (57,566)
CAP3 Assembly
Contigs(61,127)
Singlets(5,199)
Total Contigs & Singletons : 429,086 (Contigs: 61,127 Singletons:367,959)
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AnnotationTotal Sequences for Annotation (429,086)
BLASTX
24,641 have a significant match
7130 have a significant match
Remaining 404,445
Human RefSeq
BLASTNXenopus Laevis & Tropicalis Unigene
3731* have a significant match
Remaining 397,315
BLASTXNR
* BLAST not complete yet and is still running
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Two Interesting Discoveries
- Axolotl introns are large
- Genic regions contain novel genes
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Axolotl Introns are Large
Average orthologous intron size
Axolotl: 9454 bp
Human: 1938 bp
Chicken: 675 bp
Frog: 788 bp
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*
*
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Axolotl HumanBACs Introns Introns
Total interspersed: 2.32 1.77 0.38
Total retroelements: 2.24 1.67 0SINEs: 0 0 0LINEs: 0.29 0.24 0 L2/CR1/Rex 0.11 0.16 0 R1/LOA/Jockey 0 0 0 RTE/Bov-B 0.01 0.01 0 L1/CIN4 0.18 0.07 0
LTR elements: 1.95 1.43 0 Gypsy/DIRS1 1.42 0.76 0 Retroviral 0.24 0.36 0
DNA transposons: 0.08 0.10 0.38hobo-Activator <0.01 0.04 0PiggyBac 0 0 0.18Tourist/Harbinger 0.06 0.04 0
Percentage of sequences identified as repetitive
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Number of predicted non-coding RNAs
Axolotl Human
miRNAs 86 6
snRNAs 26 1
% of intron bases: 2.7% 1.2%
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So Why Are Axolotl Introns Large?
- Nucleosome or matrix attachment sites?
- Selection to moderate rates of biological processes?
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Conclusions
- Genic regions of the axolotl genome appear to be larger than they are in other vertebrates.
- Introns are larger- Evidence of novel genes
- Next step: What does the non-genic portion look like?